So Much for My Favorite 2012 Paper

posted in: Commentary | 8

Republished from Illumination.

Ask any scientist what papers truly intrigued or inspired them.  All of us have a few.

One of my favorites hit Cell Research back in summer of 2012.  In this paper, Zhang et al claimed that dietary microRNAs from rice were somehow ushered through the digestive gauntlet and modulated physiologically relevant changes in LDL, at least in mice.  MicroRNAs are a relatively recent regulatory regimen, a monkey wrench in the central dogma in of molecular biology.  These tiny runs of a 1-2 dozen nucleotides interact with RNA, leading to its degradation. They interact with RNA to change translation and bind to DNA to inspire transcriptional control.  In other words, they place a new layer of complexity into a complex process.

We know that there are 1000+ microRNAs in the human genome and probably just as many in plants.  The work by Zhang was so cool because it said that RNAs from plants could have effects on mammalian physiology.  Mice fed rice experienced changes in gene expression in their livers, apparently imparted by microRNA. It seemed consistent with what we knew about plants and their effects on blood lipoprotein levels.  The paper was really slick– it was exciting to read.

But as I reached the end I could not help but feel the skepticism oozing in.  A little back-of-the-envelope math would reveal that even with liberal estimates there’s no way that a single species of plant microRNA could be present at high enough concentrations to get through postharvest treatment, cooking, digestion, transport, and all of the other hurdles to make the process work as proposed.

The numbers I calculated were ridiculously low, impossible!

But science does have surprises.  I talked about this paper in a journal club with graduate students and remember saying, “When it is repeated or expanded, then we could get excited.”

Of course, the anti-GMO world ignited.  In a discipline founded on what we don’t know will kill us all, the specter of a tiny, rogue RNA was quite frightening.

The Atlantic’s Ari Levaux fans the fire of fear. In his estimation microRNA is clearly poison, and “our bodies are absorbing information….”. Funny, information usually does not get in very fast in my experience.

Levaux was one of many authors that used the news to drive new fears.  After all, the logical anti-GMO syllogism is that GMOs are bad,  GMO food has DNA, DNA makes RNA and RNA can be converted to microRNA.  There. Bingo! Poison!

Of course they completely fail to recognize that every bite of any animal or plant product we consume is already packed with oodles of microRNA.  But that doesn’t matter, that kind isn’t scary.

No new papers came out from Zhang and colleagues describing this paradigm-shifting find.  With time, skepticism grew.

Grow no longer.

Today my bubble was burst, as a solid refutation of the Zhang et al study hit PubMed.  In this work, Dickinson et al. could not detect the same microRNA reported by Zhang et al.

The rice microRNA miR168a was one of the most abundant microRNAs identified in the rice fed to the mice.  They also received several control diets.  Bottom line, there was almost no miR168a identified (well, there was one found in every million miRNAs).  Proper controls were done and the miRNA was detected when spiked in.  Additionally, the authors repeated Zhang’s rice feeding experiment and saw the decrease in LDL, and the changes in LDL did not depend on the availability of miR168a. The observation in Zhang et al that showed differences in the expression of the LDL Receptor Adaptor Protein were also not reproducible in this study.

The authors conclude that the physiology observed from Zhang et al 2012 was due to mice fasting, followed by feeding with rice, causing the LDL spike.

Bummer.  There always is a glimmer of hope that someone will repeat the original study and that there’s some subtle nuance that Zhang did that Dickinson et al neglected.  However, it does not appear that even a partial effect consistent with the original study was observed.  Zhang did offer a rebuttal to the Dickinson work, and it is a little more hand-wavy than hard rebuttal.  More on this later.

Many will dismiss this study because it was done with cooperation from Monsanto.  On the other hand, the other cooperator was miRagen, a company interested in small RNAs for therapies.  They have a vested interest in identifying mechanisms to orally administer miRNA and detect physiological outcomes. If they repeated Zhang et al’s work it would have been a positive finding for their company, as I’m sure they get plenty of criticism for the viability of their potential therapies.

As always, the real science rises to the top.  If the report from Dickinson is the last word, then that’s it.  If Zhang et al are hot on their claims, they will soon publish additional findings and expand on the original report.

I would absolutely love it if the Zhang et al study panned out to be true.  I always love a new crazy layer of science with new avenues to think about and how they can relate to my research.  It is fun to see that things are more complex than we guessed.  That’s good job security. However, today’s paper suggests that I’m probably going to be disappointed.

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Kevin is a public scientist that enjoys illuminating hot-button scientific issues for non-scientists using an evidence-based approach. Kevin is always uncomfortable referring to himself in the third person.

  • What I was really hoping was that someone could explain to me the evolutionary theory behind a plant that aimed to affect human cholesterol levels, and how that would be of any benefit to the plant. Also how the plant would know this.

    I mean–a plant could adapt to attract pollinators, we know that. But there’s a real reproductive reason for that.

    But if somehow rice had figured out how worried we’d be about cholesterol in 2012 and lured the humans to grow it in such abundance because of that….zowee!!

    • Samuel

      A natural selection toward humans (or their gut flora) allowing this specific mRNA to pass the digestive system would have been a more likely evolutionary explanation. I mean a bit like European had been selected for their capacity to digest lactase.

  • Mlema

    “Many will dismiss this study because it was done with cooperation from Monsanto.”

    yup. sorry. But at least you can still be excited 🙂
    Seriously, I think the rebuttal to Zhang et al is more than just hand-waving.
    Like you, I hope there will be more research done so that we’ll learn more about this.

    “what we don’t know will kill us all”
    I think you’re trying to make this sound like an overly dramatic reaction to whatever cutting edge science we’re involved in. I think it’s more likely that people who look at mistakes that we’ve made in the past think: we should be cautious and respectful of the power of our own intellect. So, it’s not “will kill us all” it’s “can kill us”.

    I’m thinking of people being sprayed down with ddt.
    Now, many people will say – “well, that was then and this is now. Now we understand those kinds of things” and they see no allegory to the fact that there is ALWAYS something we don’t know. That is the beauty of science. It’s a never-ending open book for us to read. When there are profits in employing it (as there should be) and lofty goals of human benefit (as there should be) – then we tend to get a little over-exuberant sometimes.

    Research, and caution in application. And everything will be fine (so says I) 😉

    • Kevin Folta


      I’m working on analysis of the rebuttal. Will post soon. Thanks.

  • Ari LeVaux

    “In his estimation microRNA is clearly poison”

    That’s quite a claim. Please support it with evidence. I’d be interested to know where I said, or estimated, suggested or implied, that “microRNA is clearly poison.”

    My article was about GMO regulation, not microRNA, and it’s telling how hard this is for the science blogger community to grasp. In the article I challenged Monsanto’s claim that there is “no need for, or value in testing the safety of GM foods in humans.” This caution is not the same thing as saying something is clearly poison.

    If you want toxic, check your attitude. Do you really think I don’t know that microRNA is everywhere? For the record, I know that DNA is everywhere too, and not just in the cells of GM plants.

    • Kevin Folta

      Ari, your entire article was based on the bogus reasoning of the precautionary principle and the need to have some strange non-hypothesis based level of scrutiny. I’m not opposed to testing at all, there’s a lot of it done, but it comes from a place of plausibility.

      That’s not the point. I’m sorry that you feel this is the residue of a toxic attitude.
      Maybe I’m not understanding what you meant by “Very Real Danger” in association with the original study. Okay, you didn’t say “poison” but clearly after your critical analysis the food is dangerous because of the microRNA. Po-tato, pota-to.

      The title says flat out, “The Very Real Danger of Genetically Modified Food” and I don’t see a whole lot of evidence of very real danger in the Zhang paper or otherwise. You propose mechanisms that could potentially maybe possibly could be problematic, but no more from GM than from any other food.

      Your warning beacon ignited fear across the web. You can find 1000’s of websites that link to your danger article as a credible source of the hazard.

      Over at you can even see a synthesis of your article as: “The Chinese RNA study threatens to blast a major hole in Monsanto’s claim. It means that DNA can code for microRNA, which can, in fact, be hazardous.” This is based on the Atlantic article.

      Your article about Very Real Dangers went around Facebook and other social media like wildfire. It reaffirmed the fears of an anti-intellectual movement and scared more people out of accepting safe technology that could help people and the environment.

      I do apologize if I come off with a “toxic” attitude. As an educator and scientist you made my job a little harder, that’s all. As someone that sees potentially great solutions from this technology that could help those that need it, your loose language does contribute to a growing death count. That should make me a little toxic.

      Best wishes, and I hope maybe you’ll come out with an equally visible piece about the utility of microRNA and how it might solve problems for farmers, the hungry and the environment. That would be great. Thanks.

    • Ari, thanks for stopping by. As I remember when you posted your creatively interpreted claims about GMOs, several people who understood the science, such as myself, responded to your claims. When my response to you was pointed out in this discussion, on Twitter you called me “shrill,” while other commenters thanked me for very non-combative and helpful comments. I just wanted to point this out to you since your closing argument was that people other than yourself were bringing about a toxic dialog.

      Kevin’s caption is poetic. You did tie miRNAs to disease, and talked about whether or not genetically engineered crops are poisonous or not. Whether or not you said that RNA is specifically poison doesn’t change the mood you were trying to generate in your readers, and that was to make them think it could be. Heck, the title of your post said “The Very Real Danger”!

      Personally, if I thought something was risky based on one paper, and then several analyses piled on and showed that it was wrong, then I would be elated. I would write a piece for the same news outlets saying “The Very Real Safety” of the thing I said was dangerous because of that one paper. At the very least, you could write a followup saying that the paper did not survive scrutiny, which you said yourself was a serious hurdle.

  • Anon

    “The possibility that small RNAs ingested from plant-based foods could have biological effects in humans and other mammals is currently an issue of considerable interest. It has long been known that ingested RNA from food sources is taken up by the digestive system in nematodes and insects and can control the expression of genes in those organisms. A recent report has raised the interesting possibility that a similar phenomenon occurs in humans and other mammals. This work has generated excitement because it raises the possibility of bioengineering edible plants to produce therapeutic miRNAs that could then be delivered to affected tissues by ingestion. However, it has also generated controversy, and several groups have challenged the finding. We addressed this controversy in an experiment designed to both detect a therapeutic effect of ingested miRNAs and to demonstrate their uptake in a mouse model for colon cancer. Our results indicate that tumor suppressor miRNAs designed to mimic small RNAs produced in plants were taken up by the digestive tract of ApcMin/+ mice upon ingestion, as evidenced by their higher concentration in the miRNA-treated animals. Furthermore, the ingested miRNAs were functional, as evidenced by the reduction in tumor burden in the treated mice. These results support the original finding that endogenous plant miRNAs are taken up by the mammalian digestive tract and can function to target mammalian genes, raising the intriguing prospect of using edible plants engineered to produce mammalian tumor suppressor miRNAs as an effective, nontoxic, and inexpensive chemopreventive strategy in humans.”